[gmx-users] Partial incompatibility of pdb2gmx with 4 character residue names?

Joerg Sauter joerg.sauter at mpikg.mpg.de
Thu Aug 15 15:45:56 CEST 2013


I am building a tetramer of beta(1-4) linked glucose with pdb2gmx 
(Gromacs 4.6.3). I have three residue types BGLB BGLM BGLE defined in 
the aminoacids.rtp with which I want to built the chain BGLB BGLM BGLM BGLE.

Using pdb2gmx works fine, until I link the residues via the specbond.dat 

BGLB    O4        1        BGLM    C1        1        0.147 BGLB    BGLM
BGLM    O4        1        BGLM    C1        1        0.147 BGLM    BGLM
BGLM    O4        1        BGLE    C1        1        0.147 BGLM    BGLE

In this case I get the error message:

Fatal error:
Atom HO4 in residue BGLE 4 was not found in rtp entry BGLM with 21 atoms
while sorting atoms.

Using the -debug 1 mode I found that internally (in the chain.pdb) the 
residue names get shortened to BGL thus making the residues 
indistinguishable. Therefore, pdb2gmx seems to mix up residues resulting 
in the error above. If I use residue names consisting of only 3 
characters everything works fine again.

Is this behaviour known or intended? I could not find any note on this 
in the manual and it took me some time to figure this out, so maybe 
there should be at least a warning.


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